I encountered this problem very early on with my D750 and it has been a long saga with Nikon getting it sorted out. It first manifested itself as the camera locking up on higher shutter speeds (as pointed out above, reading out as 1/4000 even when it wasn't really). That was what I sent it to Nikon for initially. They replaced the shutter and the problem still existed. Awhile later i started to get odd exposure irregularities of all sorts. including differences of opinion between the image and the data. Back it went and yet another new shutter - no change and the exposure issues got worse.
On the fourth trip back to Nikon (still under warranty, even though it had been 2 1/2 years) they finally replaced the shutter (yet again), the aperture arm and (as I suggested all along) the CPU. Presto! All problems solved and the camera is in every way better than when I first got it. 1,000 + exposures in and every one has been pretty dead-on. I even note that high ISO performance (which I use a great deal) has improved visibly. Not sue why that might be, but I'll take it!
My suspicion? A bad batch of circuit boards.